Calcium in PDB 9b3n: Human Notch-1 Egfs 20-24

The structure of Human Notch-1 Egfs 20-24, PDB code: 9b3n was solved by S.Johnson, R.Suckling, P.A.Handford, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.85 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.03, 35.08, 63.89, 99.71, 92.35, 96.86
R / Rfree (%)	17.6 / 19.8

The binding sites of Calcium atom in the Human Notch-1 Egfs 20-24 (pdb code 9b3n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Notch-1 Egfs 20-24, PDB code: 9b3n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human Notch-1 Egfs 20-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Notch-1 Egfs 20-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:21.2 occ:1.00 OD1 A:ASP907 2.2 26.5 1.0 O A:GLY925 2.3 26.3 1.0 O A:ILE908 2.3 25.1 1.0 OD1 A:ASP924 2.4 21.1 1.0 O A:HOH1151 2.5 23.8 1.0 OD2 A:ASP910 2.5 25.3 1.0 OD2 A:ASP924 2.7 26.8 1.0 CG A:ASP924 2.9 21.0 1.0 CG A:ASP907 3.4 26.8 1.0 C A:GLY925 3.5 26.4 1.0 C A:ILE908 3.5 23.3 1.0 CG A:ASP910 3.6 26.7 1.0 N A:ASP910 4.0 22.9 1.0 N A:ASN927 4.0 28.9 1.0 N A:ILE908 4.0 22.9 1.0 OD2 A:ASP907 4.0 33.1 1.0 N A:GLY925 4.1 22.8 1.0 O A:HOH1137 4.1 30.4 1.0 C A:ASP907 4.2 23.9 1.0 CB A:ASP910 4.2 25.7 1.0 CA A:ILE908 4.3 22.1 1.0 CB A:ASP924 4.3 24.1 1.0 CA A:GLY925 4.3 25.1 1.0 N A:ILE926 4.4 27.7 1.0 O A:ASP907 4.4 26.7 1.0 CA A:ILE926 4.4 28.9 1.0 O A:THR928 4.4 26.5 1.0 OD1 A:ASP910 4.5 28.9 1.0 N A:ASP909 4.5 23.6 1.0 CB A:ASP907 4.6 25.4 1.0 C A:ILE926 4.6 32.9 1.0 CA A:ASP909 4.6 24.1 1.0 O A:GLY898 4.7 28.0 1.0 CB A:ILE908 4.7 22.2 1.0 N A:THR928 4.8 24.1 1.0 O A:HOH1125 4.8 27.2 1.0 CA A:ASP910 4.8 22.8 1.0 C A:ASP924 4.8 20.9 1.0 CA A:ASP907 4.8 25.5 1.0 C A:ASP909 4.8 24.0 1.0 CA A:ASN927 4.8 28.6 1.0 CA A:ASP924 4.9 24.2 1.0

Calcium binding site 2 out of 4 in the Human Notch-1 Egfs 20-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Notch-1 Egfs 20-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:24.0 occ:1.00 O A:ILE792 2.1 28.9 1.0 O A:ASP809 2.2 25.4 1.0 OD1 A:ASN791 2.3 22.8 1.0 OD1 A:ASP808 2.3 25.7 1.0 OE2 A:GLU794 2.5 29.9 1.0 O A:HOH1147 2.5 25.1 1.0 OD2 A:ASP808 2.6 30.5 1.0 CG A:ASP808 2.8 27.6 1.0 C A:ILE792 3.3 27.0 1.0 CD A:GLU794 3.4 32.6 1.0 C A:ASP809 3.4 24.0 1.0 CG A:ASN791 3.4 25.2 1.0 OE1 A:GLU794 3.7 35.2 1.0 ND2 A:ASN791 4.1 33.7 1.0 N A:ASP809 4.1 24.3 1.0 N A:GLU794 4.1 31.4 1.0 N A:ILE792 4.1 28.5 1.0 O A:HOH1180 4.2 39.5 1.0 N A:ALA811 4.2 27.8 1.0 O A:HOH1263 4.2 35.4 1.0 C A:ASN791 4.2 28.8 1.0 CA A:ILE792 4.3 26.5 1.0 CB A:ASP808 4.3 25.8 1.0 N A:ASN793 4.3 32.5 1.0 O A:GLY812 4.3 27.5 1.0 N A:VAL810 4.3 26.8 1.0 CA A:VAL810 4.3 27.8 1.0 CA A:ASN793 4.3 31.5 1.0 CA A:ASP809 4.4 24.3 1.0 O A:ASN791 4.5 29.2 1.0 CB A:ASN791 4.7 29.5 1.0 O A:GLY782 4.7 30.9 1.0 CG A:GLU794 4.7 30.4 1.0 C A:ASP808 4.7 24.0 1.0 C A:VAL810 4.7 27.2 1.0 C A:ASN793 4.7 33.9 1.0 CB A:ILE792 4.8 26.7 1.0 CB A:GLU794 4.8 29.3 1.0 N A:GLY812 4.9 26.3 1.0 CA A:ASP808 4.9 24.3 1.0 CA A:ASN791 4.9 29.0 1.0

Calcium binding site 3 out of 4 in the Human Notch-1 Egfs 20-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Notch-1 Egfs 20-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1008 b:21.4 occ:1.00 O A:HOH1135 2.4 23.7 1.0 O A:GLY890 2.4 24.6 1.0 OD1 A:ASN886 2.4 22.8 1.0 O A:ILE870 2.4 24.0 1.0 OD1 A:ASP869 2.4 23.6 1.0 O A:THR887 2.5 26.5 1.0 OE1 A:GLU872 2.5 23.0 1.0 OD2 A:ASP869 2.9 30.8 1.0 CG A:ASP869 3.0 25.8 1.0 CG A:ASN886 3.4 25.5 1.0 C A:GLY890 3.4 21.5 1.0 CD A:GLU872 3.5 23.4 1.0 N A:GLY890 3.6 25.6 1.0 C A:ILE870 3.6 23.3 1.0 C A:THR887 3.7 29.1 1.0 OE2 A:GLU872 3.8 31.2 1.0 ND2 A:ASN886 3.8 28.9 1.0 N A:GLY889 3.9 25.4 1.0 CA A:GLY890 3.9 27.1 1.0 N A:THR887 4.0 26.6 1.0 N A:ILE870 4.2 23.3 1.0 C A:GLY889 4.2 27.9 1.0 CA A:ASN871 4.3 25.1 1.0 N A:GLU872 4.4 23.8 1.0 N A:ASN871 4.4 22.4 1.0 CA A:GLY889 4.4 26.9 1.0 CA A:THR887 4.5 26.4 1.0 CA A:ILE870 4.5 22.7 1.0 CB A:ASP869 4.5 25.0 1.0 O A:GLY860 4.5 31.3 1.0 N A:TYR891 4.6 21.9 1.0 N A:HIS888 4.7 29.8 1.0 CB A:ASN886 4.7 25.5 1.0 C A:HIS888 4.8 26.5 1.0 OG1 A:THR887 4.8 31.8 1.0 CA A:HIS888 4.8 33.0 1.0 C A:ASN886 4.9 29.2 1.0 CG A:GLU872 4.9 24.4 1.0 CA A:ASN886 4.9 27.6 1.0 C A:ASN871 4.9 23.2 1.0 CB A:ILE870 5.0 22.7 1.0

Calcium binding site 4 out of 4 in the Human Notch-1 Egfs 20-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Notch-1 Egfs 20-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1009 b:28.5 occ:0.37 OD2 A:ASP770 2.1 41.1 0.5 ND2 A:ASN755 2.2 70.0 1.0 O A:MET771 2.4 34.3 1.0 OD1 A:ASP770 2.4 33.7 0.5 CG A:ASP770 2.6 29.7 0.5 CG A:ASN755 2.8 66.3 1.0 CB A:ASN755 2.9 51.8 1.0 C A:MET771 3.6 29.3 1.0 OD1 A:ASN755 3.9 77.9 1.0 N A:MET771 4.0 28.4 1.0 CB A:ASP770 4.1 29.1 0.5 O A:HOH1311 4.1 41.7 1.0 CB A:ASP770 4.1 29.4 0.5 N A:SER773 4.2 50.8 1.0 O A:GLY774 4.3 30.7 1.0 CA A:ASN755 4.4 56.0 1.0 N A:THR772 4.4 31.0 1.0 CA A:MET771 4.5 27.2 1.0 CA A:THR772 4.5 33.7 1.0 OD1 A:ASP770 4.5 32.4 0.5 N A:GLU756 4.6 38.1 1.0 CG A:ASP770 4.6 30.1 0.5 C A:ASP770 4.7 30.5 1.0 C A:THR772 4.7 38.7 1.0 CA A:ASP770 4.8 29.3 0.5 CA A:ASP770 4.8 29.2 0.5 N A:GLY774 4.8 32.1 1.0

Z.Bo, T.Rowntree, S.Johnson, H.Nurmandi, R.Suckling, J.Hill, B.Korona, P.Weisshuhn, D.Sheppard, Y.Meng, S.Liang, E.Lowe, S.M.Lea, C.Redfield, P.A.Handford. Structural and Functional Studies of the EGF20-27 Region Reveal New Features of the Human Notch Receptor Important For Optimal Activation To Be Published.